| Parameter | Value |
|---|---|
| Project | test-gwas |
| Pipeline Version | v0.2 |
| Date | 2021-08-09 |
| Phenotype File | test/regenie_pheno_input.pheno.validated.txt |
| Phenotype | p21001_i0 |
| Covariates | COV1 |
| Regenie Output | p21001_i0.regenie.gz |
Report: GWAS analysis
.scrolling {
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}1 Project Summary
2 Phenotype Statistics
2.1 Overview
╭──────────────────────────────────────────────── skimpy summary ─────────────────────────────────────────────────╮ │ Data Summary Data Types │ │ ┏━━━━━━━━━━━━━━━━━━━┳━━━━━━━━┓ ┏━━━━━━━━━━━━━┳━━━━━━━┓ │ │ ┃ dataframe ┃ Values ┃ ┃ Column Type ┃ Count ┃ │ │ ┡━━━━━━━━━━━━━━━━━━━╇━━━━━━━━┩ ┡━━━━━━━━━━━━━╇━━━━━━━┩ │ │ │ Number of rows │ 63930 │ │ float64 │ 1 │ │ │ │ Number of columns │ 1 │ └─────────────┴───────┘ │ │ └───────────────────┴────────┘ │ │ number │ │ ┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━┳━━━━━━━┳━━━━━━━━┳━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━┓ │ │ ┃ column_name ┃ NA ┃ NA % ┃ mean ┃ sd ┃ p0 ┃ p25 ┃ p75 ┃ p100 ┃ hist ┃ │ │ ┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━╇━━━━━━━╇━━━━━━━━╇━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━━━┩ │ │ │ p21001_i0 │ 0 │ 0 │ 27 │ 5.2 │ 13 │ 24 │ 30 │ 68 │ ▂█▂ │ │ │ └─────────────────────┴───────┴──────────┴──────────┴────────┴───────┴────────┴────────┴─────────┴───────────┘ │ ╰────────────────────────────────────────────────────── End ──────────────────────────────────────────────────────╯
2.2 Phenotype distribution
3 Main results
Main results are summarised here by Manhattan and QQ plot.
Annotated SNPs represent the configured top hits (SNPs with LOG10P above 7.3) processed as follows:
- the SNP with the highest LOG10P value is selected for each gene
- the resulting SNPs are further grouped by 500kb windows and the SNP with the highest LOG10P value is then annotated in the plot with the name of the closest gene
4 Genes on top SNPs
This table summarises the closest genes for configured top hits (SNPs with LOG10P above 7.3).It reports the list of genes overlapped by top hits and for each
- the number of top hit SNPs in the gene (VARIANTS).
- the P-value of the most associated SNP (GENE_LOG10P)
- the minimum SNP-gene distance across top SNPs
| CLOSEST_GENE_NAME | CLOSEST_GENE_CHROMOSOME | CLOSEST_GENE_START | CLOSEST_GENE_END | GENE_LOG10P | VARIANTS | MIN_DISTANCE | |
|---|---|---|---|---|---|---|---|
| 17 | FTO | 16 | 53737875 | 54155853 | 29.82500 | 128 | 0 |
| 37 | SEC16B | 1 | 177893091 | 177953438 | 19.78290 | 105 | 0 |
| 15 | FAM150B | 2 | 279558 | 288851 | 16.37420 | 7 | 119862 |
| 50 | TMEM18 | 2 | 667335 | 677439 | 12.71700 | 223 | 13462 |
| 21 | MC4R | 18 | 58038564 | 58040001 | 12.14110 | 100 | 75448 |
| 6 | CAAP1 | 9 | 26840683 | 26892802 | 11.88510 | 14 | 221728 |
| 29 | PMAIP1 | 18 | 57567180 | 57571538 | 11.16240 | 71 | 160880 |
| 47 | SULT1A1 | 16 | 28616903 | 28634946 | 11.02060 | 57 | 0 |
| 45 | STX1B | 16 | 31000577 | 31021949 | 11.02020 | 6 | 0 |
| 54 | ZNF646 | 16 | 31085743 | 31095517 | 10.89830 | 2 | 0 |
| 55 | ZNF668 | 16 | 31072164 | 31085641 | 10.86730 | 10 | 0 |
| 52 | VKORC1 | 16 | 31102163 | 31107301 | 10.82340 | 2 | 388 |
| 46 | STX4 | 16 | 31044210 | 31054296 | 10.70670 | 9 | 0 |
| 28 | NUPR1 | 16 | 28548606 | 28550495 | 10.35330 | 10 | 172 |
| 3 | BCKDK | 16 | 31117428 | 31124110 | 10.28040 | 10 | 0 |
| 8 | CCDC101 | 16 | 28565236 | 28603111 | 10.19650 | 37 | 0 |
| 18 | IL27 | 16 | 28510683 | 28523372 | 10.12930 | 5 | 0 |
| 48 | SULT1A2 | 16 | 28603264 | 28608430 | 9.98147 | 12 | 0 |
| 19 | KAT8 | 16 | 31127075 | 31142714 | 9.95059 | 14 | 0 |
| 32 | PRSS8 | 16 | 31142756 | 31147083 | 9.74864 | 2 | 0 |
| 31 | PRSS36 | 16 | 31150246 | 31161415 | 9.64629 | 1 | 1105 |
| 12 | DNAJC27 | 2 | 25166505 | 25194963 | 9.61703 | 23 | 0 |
| 0 | ADCY3 | 2 | 25042038 | 25142708 | 9.60099 | 77 | 0 |
| 26 | NPIPB6 | 16 | 28353876 | 28374829 | 9.37402 | 7 | 3818 |
| 2 | ATP2A1 | 16 | 28889726 | 28915830 | 9.29087 | 11 | 0 |
| 30 | POC5 | 5 | 74969949 | 75013313 | 9.27994 | 13 | 0 |
| 13 | EIF3C | 16 | 28699879 | 28747051 | 9.20802 | 4 | 0 |
| 33 | RABEP2 | 16 | 28915742 | 28947847 | 9.06204 | 5 | 0 |
| 20 | LAT | 16 | 28996147 | 29002104 | 9.06019 | 1 | 0 |
| 23 | MON1A | 3 | 49946302 | 49967606 | 9.05754 | 6 | 0 |
| 9 | CD19 | 16 | 28943260 | 28950667 | 9.02880 | 2 | 1971 |
| 44 | SPNS1 | 16 | 28985542 | 28995869 | 9.01589 | 6 | 0 |
| 14 | EIF3CL | 16 | 28390900 | 28415200 | 8.99549 | 1 | 7658 |
| 39 | SH2B1 | 16 | 28857921 | 28885526 | 8.99470 | 2 | 0 |
| 24 | MST1R | 3 | 49924435 | 49941299 | 8.98547 | 9 | 0 |
| 5 | C6orf106 | 6 | 34555065 | 34664636 | 8.93545 | 42 | 0 |
| 25 | NFATC2IP | 16 | 28962128 | 28978418 | 8.90139 | 3 | 0 |
| 16 | FAM92A1 | 8 | 94710789 | 94743755 | 8.87419 | 1 | 134867 |
| 49 | TMEM161B | 5 | 87485450 | 87565293 | 8.77920 | 2 | 129464 |
| 1 | ANKDD1B | 5 | 74907284 | 74967671 | 8.74342 | 3 | 0 |
| 43 | SORCS3 | 10 | 106400859 | 107024993 | 8.72631 | 1 | 524597 |
| 51 | UHRF1BP1 | 6 | 34759857 | 34850915 | 8.69119 | 2 | 0 |
| 36 | SBK1 | 16 | 28303840 | 28335170 | 8.67686 | 3 | 2869 |
| 7 | CAMKV | 3 | 49895421 | 49907655 | 8.61833 | 6 | 0 |
| 41 | SNRPC | 6 | 34725183 | 34741571 | 8.37954 | 4 | 1873 |
| 4 | BCL7C | 16 | 30844947 | 30906281 | 8.34259 | 3 | 0 |
| 34 | RBM5 | 3 | 50126341 | 50156454 | 8.33358 | 5 | 0 |
| 53 | ZNF629 | 16 | 30789778 | 30798523 | 8.30771 | 1 | 22343 |
| 35 | RBM6 | 3 | 49977440 | 50137478 | 8.29983 | 51 | 0 |
| 27 | NPIPB8 | 16 | 28648975 | 28670003 | 8.29261 | 3 | 0 |
| 42 | SNX11 | 17 | 46180719 | 46200436 | 8.28665 | 1 | 0 |
| 11 | CTD-2330K9.3 | 3 | 49941278 | 49954370 | 8.23756 | 1 | 0 |
| 22 | MIB2 | 1 | 1550795 | 1565990 | 8.22438 | 6 | 0 |
| 40 | SKAP1 | 17 | 46210802 | 46507637 | 8.17291 | 2 | 0 |
| 38 | SETD1A | 16 | 30968615 | 30996437 | 8.09561 | 2 | 0 |
| 10 | CLN3 | 16 | 28477983 | 28506896 | 8.05179 | 1 | 0 |
5 Top Loci
This table lists top associated loci after clumping using plink. The minimum log10 p-value for index SNPs is 7.3
| CHR | SNP | P | N | POS | KB | RANGES | |
|---|---|---|---|---|---|---|---|
| 0 | 16 | rs56094641_A_G | 1.496000e-30 | 116 | chr16:53797908..53845487 | 47.580 | [FTO] |
| 1 | 1 | rs539515_A_C | 1.649000e-20 | 71 | chr1:177793822..177913519 | 119.698 | [SEC16B] |
| 2 | 16 | rs12446228_A_G | 1.673000e-17 | 14 | chr16:53797565..53848561 | 50.997 | [FTO] |
| 3 | 2 | rs62106258_T_C | 4.225000e-17 | 7 | chr2:408713..466003 | 57.291 | [] |
| 4 | 16 | 16:53825987_CA_C_CA_C | 4.109000e-14 | 1 | chr16:53825987..53825987 | 0.001 | [FTO] |
| 5 | 2 | rs6744653_A_G | 1.919000e-13 | 238 | chr2:600575..653874 | 53.300 | [TMEM18] |
| 6 | 18 | rs35614134_A_AC | 7.226000e-13 | 182 | chr18:57732418..57914679 | 182.262 | [] |
| 7 | 9 | rs11791087_C_G | 1.303000e-12 | 15 | chr9:26586297..26618114 | 31.818 | [] |
| 8 | 1 | rs531385_T_C | 1.540000e-12 | 23 | chr1:177849243..177922471 | 73.229 | [SEC16B] |
| 9 | 16 | rs7187961_T_C | 3.350000e-12 | 1 | chr16:53826034..53826034 | 0.001 | [FTO] |
| 10 | 16 | 16:28621572_GT_G_GT_G | 9.537000e-12 | 317 | chr16:28372911..28871200 | 498.290 | [APOBR,ATP2A1,ATXN2L,CCDC101,CLN3,EIF3C,EIF3CL... |
| 11 | 16 | rs34898535_C_T | 9.546000e-12 | 80 | chr16:30820866..31149142 | 328.277 | [BCKDK,BCL7C,CTF1,FBXL19,FBXL19-AS1,HSD3B7,KAT... |
| 12 | 18 | rs17700633_G_A | 1.628000e-10 | 75 | chr18:57916904..58017249 | 100.346 | [MC4R] |
| 13 | 2 | rs10865321_T_C | 2.415000e-10 | 173 | chr2:25075281..25321768 | 246.488 | [ADCY3,DNAJC27,DNAJC27-AS1,EFR3B] |
| 14 | 1 | 1:177890130_CT_C_CT_C | 2.525000e-10 | 3 | chr1:177848153..177890130 | 41.978 | [SEC16B] |
| 15 | 16 | rs2466826_G_A | 4.226000e-10 | 33 | chr16:28330968..28582849 | 251.882 | [APOBR,CCDC101,CLN3,EIF3C,EIF3CL,IL27,MIR6862-... |
| 16 | 16 | rs11642449_C_T | 5.118000e-10 | 70 | chr16:28809610..29001460 | 191.851 | [ATP2A1,ATXN2L,CD19,LAT,LOC100289092,MIR4517,M... |
| 17 | 5 | rs6874626_G_A | 5.249000e-10 | 108 | chr5:74934009..75038901 | 104.893 | [ANKDD1B,POC5] |
| 18 | 3 | rs7634084_A_T | 7.600000e-10 | 277 | chr3:49734229..50197097 | 462.869 | [AMIGO3,APEH,CAMKV,CDHR4,FAM212A,GMPPB,IP6K1,M... |
| 19 | 16 | 16:28988633_TA_T_TA_T | 9.641000e-10 | 1 | chr16:28988633..28988633 | 0.001 | [LAT,MIR4517,NFATC2IP,SPNS1] |
| 20 | 6 | rs2744948_A_G | 1.160000e-09 | 451 | chr6:34548206..34832661 | 284.456 | [ANKS1A,C6orf106,SNRPC,SPDEF,TAF11,UHRF1BP1] |
| 21 | 8 | rs528627779_C_A | 1.336000e-09 | 1 | chr8:94575923..94575923 | 0.001 | [LINC00535] |
| 22 | 1 | rs10913446_T_C | 1.540000e-09 | 29 | chr1:177791704..177819166 | 27.463 | [] |
| 23 | 5 | rs11424167_T_TA | 1.663000e-09 | 75 | chr5:87449984..87840688 | 390.705 | [LINC00461,LOC102546226,TMEM161B,TMEM161B-AS1] |
| 24 | 10 | rs555419279_A_C | 1.878000e-09 | 1 | chr10:107549590..107549590 | 0.001 | [] |
| 25 | 1 | rs11583928_T_C | 2.110000e-09 | 2 | chr1:177922617..177924529 | 1.913 | [SEC16B] |
| 26 | 1 | rs12135579_C_T | 2.213000e-09 | 7 | chr1:177770097..177779502 | 9.406 | [] |
| 27 | 1 | rs10913468_C_G | 2.769000e-09 | 1 | chr1:177913402..177913402 | 0.001 | [SEC16B] |
| 28 | 17 | rs12939514_T_C | 5.168000e-09 | 117 | chr17:46039553..46442786 | 403.234 | [CBX1,CDK5RAP3,COPZ2,LOC100506325,MIR152,MIR12... |
| 29 | 1 | rs74892851_C_A | 5.965000e-09 | 29 | chr1:1529994..1601052 | 71.059 | [C1orf233,CDK11B,MIB2,MMP23A,MMP23B,SLC35E2B,S... |
| 30 | 9 | rs10757617_C_G | 9.523000e-09 | 16 | chr9:26583608..26628485 | 44.878 | [] |
| 31 | 7 | rs34982641_G_A | 1.360000e-08 | 50 | chr7:75038408..75196531 | 158.124 | [HIP1,NSUN5P1,PMS2P3,POM121C,SPDYE5,TRIM73,TRI... |
| 32 | 6 | 6:34708410_GGGGAGTAAGTACAAGGTTGCTAGTCT_G_GGGGA... | 1.383000e-08 | 5 | chr6:34580221..34801188 | 220.968 | [C6orf106,SNRPC,UHRF1BP1] |
| 33 | 19 | rs34783010_G_T | 1.493000e-08 | 10 | chr19:46179043..46202172 | 23.130 | [FBXO46,GIPR,MIR642A,MIR642B,QPCTL,SNRPD2] |
| 34 | 9 | rs139480803_C_T | 1.578000e-08 | 2 | chr9:26494530..26586507 | 91.978 | [] |
| 35 | 12 | 12:24836332_ATACAT_A_ATACAT_A | 1.628000e-08 | 1 | chr12:24836332..24836332 | 0.001 | [] |
| 36 | 18 | rs9945307_A_G | 1.642000e-08 | 30 | chr18:57730096..57801689 | 71.594 | [] |
| 37 | 2 | rs199992729_T_C | 1.737000e-08 | 73 | chr2:100637788..100797912 | 160.125 | [AFF3] |
| 38 | 2 | rs2058625_A_T | 1.748000e-08 | 5 | chr2:58960544..59042342 | 81.799 | [LINC01122] |
| 39 | 2 | rs12468708_C_A | 1.784000e-08 | 53 | chr2:58866584..58999505 | 132.922 | [LINC01122] |
| 40 | 1 | rs144847043_G_A | 1.946000e-08 | 1 | chr1:177830321..177830321 | 0.001 | [] |
| 41 | 16 | 16:28737148_CT_C_CT_C | 2.036000e-08 | 1 | chr16:28737148..28737148 | 0.001 | [EIF3C,EIF3CL,MIR6862-1,MIR6862-2] |
| 42 | 16 | 16:28864262_CAT_C_CAT_C | 2.770000e-08 | 1 | chr16:28864262..28864262 | 0.001 | [ATXN2L,MIR4721,SH2B1,TUFM] |
| 43 | 6 | rs765469261_T_TTC | 3.370000e-08 | 22 | chr6:34553048..34828553 | 275.506 | [C6orf106,SNRPC,TAF11,UHRF1BP1] |
| 44 | 4 | rs527434584_A_AT | 4.162000e-08 | 1 | chr4:137887773..137887773 | 0.001 | [] |
| 45 | 9 | rs187181201_T_C | 4.372000e-08 | 1 | chr9:127668244..127668244 | 0.001 | [GOLGA1] |
| 46 | 1 | rs10913483_C_A | 4.389000e-08 | 35 | chr1:177938437..177978859 | 40.423 | [LOC730102,SEC16B] |
| 47 | 16 | rs12922786_T_C | 4.814000e-08 | 78 | chr16:30150001..30343236 | 193.236 | [BOLA2,BOLA2B,CD2BP2,CORO1A,LOC388242,LOC60672... |
5.1 Locus 1 - rs56094641_A_G
5.2 Locus 2 - rs539515_A_C
5.3 Locus 3 - rs12446228_A_G
5.4 Locus 4 - rs62106258_T_C
5.5 Locus 5 - 16:53825987_CA_C_CA_C
6 Validation and Logs
6.1 Phenotype File Validation
| Name | Value | |
|---|---|---|
| 0 | Samples | 63930 |
6.2 Covariate File Validation
| Name | Value | |
|---|---|---|
| 0 | Samples | 60724 |
6.3 Regenie Step 1 Log
| Name | Value | |
|---|---|---|
| 0 | Regenie Version | v3.1.3.gz |
| 1 | Variants total (*.bim) | 417948 |
| 2 | Number of defined phenotypes | 1 |
| 3 | Phenotyped individuals total | 60724 |
| 4 | Number of defined covariates | 21 |
| 5 | Phenotyped individuals used | 60724 |
| 6 | Regenie Call | --step 1 --bed step1_dataset_autosomes_QCe... |
6.4 Regenie Step 2 Log
| Name | Value | |
|---|---|---|
| 0 | Regenie Version | v3.1.3.gz |
| 1 | MAC limit | 50 |
| 2 | Imputation info score limit | 0.0 |
| 3 | Number of defined phenotypes | 1 |
| 4 | Phenotyped individuals total | 60608 |
| 5 | Number of defined covariates | 21 |
| 6 | Phenotyped individuals used | 60608 |
| 7 | Variants ignored (low MAC or low info score) | 49064 |
| 8 | Variants used (\*.bgen or \*.pvar) | 42795932 |
| 9 | Regenie Call | --step 2 --bgen step2_dataset_autosomes.ma... |
This report has been created with nf-fast-regenie v0.2, a nextflow pipeline developed by Edoardo Giacopuzzi at the Human Technopole Foundation, Milan, Italy. Plots are generated using gwaslab package